We have too many quality midfielders and one quality (and healthy) left fullback so I'd let Raphael stay in defense and put Gomes or Adrien there depending on who we play. I don't think André Silva is ready to start either and after Nani's Euros can we really take him out? So something like this:
Ronaldo - Nani
João Mário - Gomes/Adrien - Bernardo Silva
Danilo
Raphael Guerreiro - Pepe - Fonte - Nelson Semedo
Patrício
Gelson, super sub Quaresma and André Silva ready to come off the bench if we need a goal, William if we need to park the bus, Renato/Gomes/Adrien/Moutinho if we need to refresh the midfield and Éder if we need a miracle. I think we have all the options we could hope for and with Nelson Semedo and Bernardo Silva we'll be solving two of our biggest problems from the Euros: right back and lack of creativity from midfield.